Contacts of the helix formed by residues 195 - 200 (chain E) in PDB entry 4LML
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 195 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247D LYS* 3.3 31.6 - - - +
248D ALA* 3.4 29.6 + - - -
192E GLN 4.2 2.1 + - - -
194E PHE* 1.3 82.8 - - - +
196E TYR* 1.3 63.8 + - - +
198E PRO* 3.2 10.8 - - - +
199E ASN* 2.5 42.6 + - - +
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Residues in contact with TYR 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D LYS* 3.8 35.9 - - + +
118E TYR* 3.2 33.6 + + - -
119E PRO* 3.9 29.8 - - + -
120E PHE* 6.2 0.2 - - + -
191E ARG* 3.9 19.5 + - - -
192E GLN 3.6 14.8 - - - -
193E TYR* 3.4 23.8 - - - +
194E PHE 2.9 0.4 + - - -
195E SER* 1.3 81.3 + - - +
197E ILE* 1.3 60.3 + - + +
199E ASN* 4.3 4.5 - - - -
200E ILE* 2.8 41.8 + - + +
201E ILE* 2.8 19.2 + - + -
241E VAL* 6.5 0.7 - - + -
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Residues in contact with ILE 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D PHE* 5.9 0.9 - - + -
120E PHE* 4.9 8.3 - - + -
193E TYR* 3.1 43.5 - - + +
194E PHE* 2.9 25.0 + - + +
196E TYR* 1.3 73.4 - - + +
198E PRO* 1.3 73.2 - - + +
199E ASN 3.1 2.3 + - - -
201E ILE* 3.8 17.3 - - + -
202E LEU* 2.9 57.0 + - + +
203E PRO* 3.3 0.2 - - - +
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Residues in contact with PRO 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ASN* 4.9 1.6 - - - +
251D MET* 5.0 10.8 - - + -
255D GLY 4.7 7.6 - - - +
258D ILE* 5.3 2.5 - - - +
259D PHE* 4.2 40.4 - - + +
262D TYR* 4.6 6.2 - - - -
194E PHE* 3.0 47.3 - - + +
195E SER* 3.2 11.7 - - - +
197E ILE* 1.3 84.0 - - + +
199E ASN* 1.3 60.3 + - - +
203E PRO* 3.1 17.8 - - + +
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Residues in contact with ASN 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ASN* 4.0 21.4 + - - +
242D GLU* 3.6 32.6 - - - +
247D LYS* 3.7 12.3 - - - +
255D GLY* 5.7 4.2 - - - +
258D ILE* 5.3 3.5 - - - +
195E SER* 2.5 40.5 + - - +
196E TYR* 4.3 0.7 - - - -
197E ILE 3.1 0.6 - - - -
198E PRO* 1.3 84.3 - - - +
200E ILE* 1.3 67.5 + - + +
203E PRO* 3.2 15.6 - - - +
237E PHE* 3.5 14.0 - - - -
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Residues in contact with ILE 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D GLU* 3.3 27.4 - - - +
196E TYR* 2.8 34.0 + - + +
199E ASN* 1.3 80.6 - - + +
201E ILE* 1.3 74.8 + - + +
202E LEU 3.7 0.2 - - - -
203E PRO* 3.5 1.1 - - - +
204E MET* 3.0 39.9 + - + +
237E PHE* 4.0 16.9 - - + -
240E LEU* 3.9 20.9 - - + -
241E VAL* 3.8 27.8 - - + -
254E THR* 5.6 6.5 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il